PDB-3zcn: Fic protein from SHEWANELLA ONEIDENSIS in complex with ATP

ID or keywords:

Entry

Database: PDB / ID: 3zcn

Title

Fic protein from SHEWANELLA ONEIDENSIS in complex with ATP

Components

ADENOSINE MONOPHOSPHATE-PROTEIN TRANSFERASE SOFIC

Keywords

TRANSFERASE / AMPYLATION / ADENYLYLATION

Function / homology

Function and homology information

AMPylase activity / protein adenylylation / protein adenylyltransferase / magnesium ion binding / protein homodimerization activity / ATP binding
Similarity search - Function

Biological species

SHEWANELLA ONEIDENSIS (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.7 Å

Authors

Goepfert, A. / Schirmer, T.

Citation

Journal: Plos One / Year: 2013
Title: Conserved Inhibitory Mechanism and Competent ATP Binding Mode for Adenylyltransferases with Fic Fold.
Authors: Goepfert, A. / Stanger, F.V. / Dehio, C. / Schirmer, T.

History

Deposition	Nov 21, 2012	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jun 19, 2013	Provider: repository / Type: Initial release
Revision 1.1	Feb 12, 2014	Group: Database references
Revision 1.2	Dec 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	3zcn.cif.gz	328.9 KB	Display	PDBx/mmCIF format
PDB format	pdb3zcn.ent.gz	266.7 KB	Display	PDB format
PDBx/mmJSON format	3zcn.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zc/3zcn ftp://data.pdbj.org/pub/pdb/validation_reports/zc/3zcn	HTTPS FTP

-
Related structure data

Related structure data	3zc7C 3zcbC 3zecC 3zlmC 3eqxS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	2vqs-2 1zmx-1 2jj8-1 6orf-1 5jd3-10 2vp9-2 3ky8-d 3un7-2 5lw0-d 1zmx-4 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: ADENOSINE MONOPHOSPHATE-PROTEIN TRANSFERASE SOFIC

B: ADENOSINE MONOPHOSPHATE-PROTEIN TRANSFERASE SOFIC

hetero molecules

87.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: ADENOSINE MONOPHOSPHATE-PROTEIN TRANSFERASE SOFIC

hetero molecules

defined by author&software
43.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: ADENOSINE MONOPHOSPHATE-PROTEIN TRANSFERASE SOFIC

hetero molecules

defined by author&software
43.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	37.790, 164.910, 70.230
Angle α, β, γ (deg.)	90.00, 94.43, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	ADENOSINE MONOPHOSPHATE-PROTEIN TRANSFERASE SOFIC / FIC DOMAIN CONTAINING TRANSCRIPTION REGULATOR / AMPYLATOR SOFIC Mass: 43141.379 Da / Num. of mol.: 2 / Fragment: FIC DOMAIN, RESIDUES 2-372 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) SHEWANELLA ONEIDENSIS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q8E9K5, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#2: Chemical	ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₆N₅O₁₃P₃ / Comment: ATP, energy-carrying molecule*YM
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 981 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

Crystal	Density Matthews: 2.6 Å³/Da / Density % sol: 52.7 % / Description: NONE
Crystal grow	pH: 7.1 / Details: 21%W/V PEG 3350, 0.2M NAF PH 7.1

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.979
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 14, 2011
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 1.7→82.46 Å / Num. obs: 93236 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / B_iso Wilson estimate: 17.31 Å² / R_merge(I) obs: 0.04 / Net I/σ(I): 22.78
Reflection shell	Resolution: 1.7→1.8 Å / Redundancy: 3.4 % / R_merge(I) obs: 0.41 / Mean I/σ(I) obs: 3.46 / % possible all: 97.7

-
Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE)	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3EQX

3eqx

Resolution: 1.7→14.992 Å / SU ML: 0.17 / σ(F): 1.99 / Phase error: 21.32 / Stereochemistry target values: ML
Details: LOCAL TORSION-ANGLE NCS RESTRAINTS AS IMPLEMENTED IN PHENIX HAVE BEEN APPLIED FOR REFINEMENT

	R_factor	Num. reflection	% reflection
R_free	0.2022	4655	5 %
R_work	0.1663	-	-
obs	0.1681	93100	99.48 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 2.8553 Å² / k_sol: 1.0985 e/Å³

Displacement parameters

B_iso mean: 23.5 Å²

Refinement step

Cycle: LAST / Resolution: 1.7→14.992 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5912	0	62	981	6955

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	6163
X-RAY DIFFRACTION	f_angle_d	1.128	8421
X-RAY DIFFRACTION	f_dihedral_angle_d	17.108	2365
X-RAY DIFFRACTION	f_chiral_restr	0.073	974
X-RAY DIFFRACTION	f_plane_restr	0.006	1068

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.7-1.7193	0.2965	149	0.2471	2837	X-RAY DIFFRACTION	94
1.7193-1.7395	0.2957	146	0.232	2775	X-RAY DIFFRACTION	97
1.7395-1.7607	0.2645	156	0.232	2953	X-RAY DIFFRACTION	99
1.7607-1.7829	0.2855	154	0.218	2922	X-RAY DIFFRACTION	99
1.7829-1.8064	0.2341	158	0.2197	3010	X-RAY DIFFRACTION	100
1.8064-1.8311	0.2471	152	0.2112	2894	X-RAY DIFFRACTION	100
1.8311-1.8572	0.2722	155	0.2026	2939	X-RAY DIFFRACTION	100
1.8572-1.8848	0.2762	158	0.2022	3001	X-RAY DIFFRACTION	100
1.8848-1.9142	0.261	154	0.2007	2923	X-RAY DIFFRACTION	100
1.9142-1.9456	0.2519	156	0.1993	2967	X-RAY DIFFRACTION	100
1.9456-1.979	0.2738	156	0.1929	2961	X-RAY DIFFRACTION	100
1.979-2.0149	0.2177	155	0.1886	2941	X-RAY DIFFRACTION	100
2.0149-2.0536	0.2342	153	0.1778	2910	X-RAY DIFFRACTION	100
2.0536-2.0954	0.2276	158	0.1675	3006	X-RAY DIFFRACTION	100
2.0954-2.1408	0.208	155	0.1704	2937	X-RAY DIFFRACTION	100
2.1408-2.1905	0.2334	155	0.165	2964	X-RAY DIFFRACTION	100
2.1905-2.2451	0.2406	155	0.163	2940	X-RAY DIFFRACTION	100
2.2451-2.3056	0.1939	155	0.161	2947	X-RAY DIFFRACTION	100
2.3056-2.3732	0.199	158	0.1617	2998	X-RAY DIFFRACTION	100
2.3732-2.4495	0.1982	154	0.155	2912	X-RAY DIFFRACTION	100
2.4495-2.5366	0.1979	157	0.1503	2990	X-RAY DIFFRACTION	100
2.5366-2.6376	0.2025	154	0.1536	2928	X-RAY DIFFRACTION	100
2.6376-2.757	0.201	158	0.1635	2998	X-RAY DIFFRACTION	100
2.757-2.9013	0.2245	156	0.1645	2970	X-RAY DIFFRACTION	100
2.9013-3.0817	0.1966	155	0.1753	2944	X-RAY DIFFRACTION	100
3.0817-3.3172	0.1981	156	0.1664	2964	X-RAY DIFFRACTION	100
3.3172-3.6467	0.1797	156	0.1575	2961	X-RAY DIFFRACTION	100
3.6467-4.1644	0.1886	158	0.1416	2999	X-RAY DIFFRACTION	100
4.1644-5.2099	0.1339	156	0.1361	2963	X-RAY DIFFRACTION	100
5.2099-14.9926	0.1424	157	0.1498	2991	X-RAY DIFFRACTION	99

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	1.5638	-0.6649	0.5166	1.7974	-1.1458	0.9291	-0.0086	0.2533	0.0164	-0.8486	-0.1677	0.4156	-0.1649	-0.2459	-0.0667	0.4324	0.0832	-0.1914	0.1815	0.0042	0.1742	-16.4805	58.6194	-45.3894
2	0.4929	0.1971	-0.0101	1.9766	-0.0299	1.6785	0.0174	-0.0847	0.0912	0.2888	-0.0665	0.0124	-0.2062	0.0194	0.0387	0.0829	0.0077	-0.0188	0.094	-0.001	0.1073	-6.3669	57.8637	-15.7888
3	6.124	2.7862	0.843	3.7088	0.7343	3.5343	-0.0778	-0.2142	0.0998	0.1842	-0.0249	0.4096	-0.3317	-0.3418	0.0846	0.1541	0.0719	0.0374	0.1284	-0.0018	0.1576	-16.0386	64.2335	-14.8425
4	0.5899	-0.2806	0.9602	1.471	-0.6877	3.5916	-0.2123	-0.115	-0.0237	0.1776	0.0133	0.5601	-0.5306	-0.7302	0.1172	0.1886	0.1067	0.0127	0.2323	-0.0421	0.3177	-22.8709	68.5759	-24.9559
5	1.6368	-0.2576	-0.0347	1.1636	0.5604	0.7495	0.0731	-0.0792	0.2216	-0.4472	-0.0881	0.6294	-0.1189	-0.1091	-0.0163	0.1335	0.0426	-0.092	0.1224	-0.0285	0.2442	-16.9441	61.9345	-36.2287
6	1.0866	-0.1719	-0.5523	2.6188	-1.1301	2.4219	-0.0471	-0.034	0.0243	-0.1086	-0.0438	0.0887	-0.0544	0.0216	0.083	0.0626	0.0187	-0.0334	0.0704	-0.0199	0.1009	-9.3587	59.8472	-29.0494
7	1.4513	-0.2755	2.2078	1.2188	-0.6799	6.3161	0.0673	-0.0761	-0.0375	0.147	-0.0664	-0.0749	0.1043	0.3099	-0.0109	0.0495	-0.0067	-0.0054	0.0892	0.0135	0.1197	-0.2591	50.2614	-14.8176
8	1.1212	-0.4177	-0.3109	1.7269	0.3618	3.4141	0.0048	-0.2187	0.0906	0.5866	-0.0326	-0.0422	-0.4342	0.0366	0.0302	0.3848	-0.0613	-0.0282	0.2168	0.0036	0.1515	-1.9802	59.6416	5.3021
9	1.8042	-0.5219	-0.1145	2.0679	1.3757	1.144	-0.0949	0.2577	-0.0745	-0.671	-0.1734	-0.4125	0.232	0.2415	-0.0475	0.3564	0.0798	0.1914	0.179	0.0151	0.1604	3.169	20.363	-43.9215
10	0.5254	0.294	-0.2185	1.6855	0.0255	1.8548	-0.0108	-0.0869	-0.0722	0.1885	-0.0576	0.0048	0.1916	0.01	0.0574	0.0543	0.0235	0.0058	0.1	0.0074	0.1057	-7.2087	22.1602	-14.9912
11	4.9061	2.4175	-1.0507	3.4694	-0.3249	2.6541	-0.0449	-0.2165	-0.1083	0.1457	-0.1235	-0.2778	0.3389	0.3834	0.0986	0.1113	0.0528	-0.0393	0.1436	0.0285	0.1298	2.3759	15.8134	-13.6635
12	0.1968	-0.3513	-0.5549	1.4855	0.3825	2.0185	-0.1734	-0.0896	-0.095	0.2469	0.0578	-0.5173	0.3873	0.7458	0.0694	0.183	0.1335	0.0021	0.2906	0.0609	0.2617	9.432	11.1357	-23.495
13	1.6644	0.5448	0.4675	1.0616	-0.3883	0.976	0.1451	-0.0625	-0.3591	-0.4199	-0.2691	-0.6316	0.397	0.218	0.0964	0.1409	0.0689	0.124	0.1615	0.0646	0.3726	4.0569	11.2019	-36.0193
14	0.8841	0.0608	0.3292	2.3855	0.3804	1.7277	-0.0291	-0.0222	-0.0206	-0.1108	-0.0431	-0.1272	0.0472	0.0414	0.0664	0.0479	0.0338	0.0181	0.0916	0.0206	0.0928	-2.3271	21.2121	-29.5657
15	0.773	-0.2467	-1.7399	1.2724	0.6893	7.9816	0.0635	-0.0296	0.0215	0.1013	-0.0413	0.0892	-0.3356	-0.3556	-0.0162	0.0411	0.0164	-0.0103	0.0986	-0.0008	0.1001	-13.2555	29.7768	-14.3687
16	2.4585	-0.4586	0.5773	2.2335	-0.4491	3.9488	0.0146	-0.2761	-0.1072	0.5047	-0.0543	-0.0092	0.2247	0.1572	0.0359	0.2119	-0.0295	-0.0028	0.1709	0.0176	0.1043	-11.7686	21.1754	5.8705

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN A AND (RESID 2 THROUGH 27 )
2	X-RAY DIFFRACTION	2	CHAIN A AND (RESID 28 THROUGH 93 )
3	X-RAY DIFFRACTION	3	CHAIN A AND (RESID 94 THROUGH 115 )
4	X-RAY DIFFRACTION	4	CHAIN A AND (RESID 116 THROUGH 141 )
5	X-RAY DIFFRACTION	5	CHAIN A AND (RESID 142 THROUGH 197 )
6	X-RAY DIFFRACTION	6	CHAIN A AND (RESID 198 THROUGH 252 )
7	X-RAY DIFFRACTION	7	CHAIN A AND (RESID 253 THROUGH 292 )
8	X-RAY DIFFRACTION	8	CHAIN A AND (RESID 293 THROUGH 370 )
9	X-RAY DIFFRACTION	9	CHAIN B AND (RESID 3 THROUGH 27 )
10	X-RAY DIFFRACTION	10	CHAIN B AND (RESID 28 THROUGH 93 )
11	X-RAY DIFFRACTION	11	CHAIN B AND (RESID 94 THROUGH 115 )
12	X-RAY DIFFRACTION	12	CHAIN B AND (RESID 116 THROUGH 141 )
13	X-RAY DIFFRACTION	13	CHAIN B AND (RESID 142 THROUGH 176 )
14	X-RAY DIFFRACTION	14	CHAIN B AND (RESID 177 THROUGH 252 )
15	X-RAY DIFFRACTION	15	CHAIN B AND (RESID 253 THROUGH 292 )
16	X-RAY DIFFRACTION	16	CHAIN B AND (RESID 293 THROUGH 370 )

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi